Align Acetate--CoA ligase CCL3; HlCCL3; 2-methylbutanoate--CoA ligase CCL4; 2-methylpropanoate--CoA ligase CCL4; Butanoate--CoA ligase CCL3; Hexanoate--CoA ligase CCL3; Isovalerate--CoA ligase CCL3; Pentanoate--CoA ligase CCL3; Propionate--CoA ligase CCL3; EC 6.2.1.1; EC 6.2.1.-; EC 6.2.1.17 (characterized)
to candidate Ac3H11_191 3-methylmercaptopropionyl-CoA ligase (DmdB)
Query= SwissProt::M4IS88 (568 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_191 Length = 548 Score = 580 bits (1496), Expect = e-170 Identities = 289/553 (52%), Positives = 371/553 (67%), Gaps = 15/553 (2%) Query: 11 LPKNAANYTALTPLWFLERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIGL 70 LP+ AN+ L+PL F+ER A V+P R +++HG+ TW QTY RCRQ ASAL IG Sbjct: 9 LPRTEANFAPLSPLSFIERTAEVYPDRLAIVHGTLRQTWAQTYARCRQLASALVQAGIGK 68 Query: 71 GSTVAVIAPNVPALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFFS 130 TVAV+ PN P + EAHF VPMAGAV+N +N RL+ IAF+L H A V+VD EF Sbjct: 69 NDTVAVMLPNTPPMVEAHFGVPMAGAVLNALNTRLDPEAIAFMLDHGEAKVVLVDPEFTG 128 Query: 131 LAEEALKILAQESKSHYKPPLLVVIGDESCDPKTLEYALKTGAIEYEKFLEGGDPEFDWK 190 +AL + ++ P ++ + D P G +Y+ F+ GD F W+ Sbjct: 129 TMAKALAL-----RTGTTPIRVIEVQDALYGPAVQGL----GGTDYDAFVASGDATFAWR 179 Query: 191 PPEDEWQSISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHCN 250 P DEW +I+L YTSGTT +PKGVV HRGA ++S + W + + A+YLWTLPMFHCN Sbjct: 180 LPADEWDAIALNYTSGTTGNPKGVVYHHRGAASNAISNVLEWDMPKHAVYLWTLPMFHCN 239 Query: 251 GWCYTWGMAAFCGTNICLRQVTAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIPL 310 GWC+ W +AA G N+CLR+V A+ ++ AI +GVTH+C AP+V +VNAP E + Sbjct: 240 GWCFPWTIAARAGVNVCLRRVDAQAIFDAIRTHGVTHYCGAPIVHGLLVNAP-EAMKAGI 298 Query: 311 PHLVHVMTAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQAR 370 P V M AGAAPP S++ M + GF + H YGL+E YGP+T+CA WD L ++AR Sbjct: 299 PAGVKAMVAGAAPPASMIEGMEKMGFDLTHVYGLTEVYGPATVCAKHEAWDQLDIGERAR 358 Query: 371 LNARQGVRYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESFAD 430 LNARQGVRY + V+D +TM+PVP DG TMGEI+ +GN MKGYLKNPKA EE+FA Sbjct: 359 LNARQGVRYHLERDVRVLDPETMQPVPQDGETMGEIMFKGNIAMKGYLKNPKATEEAFAG 418 Query: 431 GWFHSGDLAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPDE 490 GWFHSGDLAV++PDGYI+IKDRSKDIIISGGENISS+EVE+ LY HP VL +VVA+PD Sbjct: 419 GWFHSGDLAVQYPDGYIKIKDRSKDIIISGGENISSIEVEDVLYRHPDVLAAAVVAKPDA 478 Query: 491 RWGESPCAFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVFGPLPKTATGKIQK 550 +WGE+PCAFV L K+ + EDI+ CK + + VP++VVFG LPKT+TGKIQK Sbjct: 479 KWGETPCAFVEL-----KAGAEATPEDIVAHCKKHLAGFKVPRAVVFGELPKTSTGKIQK 533 Query: 551 HVLRAKAKEMGAL 563 LR A A+ Sbjct: 534 FELRKLAGSAAAI 546 Lambda K H 0.318 0.134 0.415 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 926 Number of extensions: 31 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 568 Length of database: 548 Length adjustment: 36 Effective length of query: 532 Effective length of database: 512 Effective search space: 272384 Effective search space used: 272384 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory